GEA Analysis

1. LFMM

1.1 Individual sampling

1.1.1 Summary plots

K

walk(K_plots, grid.arrange)

TPRCOMBO

walk(TPR_plots, grid.arrange)

FDRCOMBO

walk(FDR_plots, grid.arrange)

### TOTALN

walk(TOTALN_plots, grid.arrange)

1.1.2 Model summaries

lfmm_ind <- 
  lfmm_ind %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge") %>%
  filter(K_selection == "tracy.widom")

run_lmer(lfmm_ind, "TPRCOMBO", filepath = here(p4path, "LFMM_individual_TPR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	0.0002	3.8849	3.8849	1	15.3180K	374.16691	2.2 × 10−82***
sampstrat	0.1243	0.8737	0.2912	3	15.3180K	28.04836	4.4 × 10−18***
K	0.0338	4.3713	4.3713	1	15.3180K	421.01179	2.6 × 10−92***
m	0.0358	4.9147	4.9147	1	15.3180K	473.35104	2.2 × 10−103***
phi	0.1114	47.5572	47.5572	1	15.3180K	4580.39346	0.0***
H	0.1150	50.6577	50.6577	1	15.3180K	4879.02098	0.0***
r	−0.0183	1.2795	1.2795	1	15.3180K	123.23782	1.6 × 10−28***
*** p < 0.001

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - G	−0.0014	0.0023	−0.5948	0.9336946
EG - R	0.0030	0.0023	1.2961	0.5653833
EG - T***	0.0176	0.0023	7.5567	2.7 × 10−13***
G - R	0.0044	0.0023	1.8908	0.2319131
G - T***	0.0190	0.0023	8.1508	5.0 × 10−14***
R - T***	0.0146	0.0023	6.2616	2.3 × 10−9***
*** p < 0.001

run_lmer(lfmm_ind, "FDRCOMBO", filepath = here(p4path, "LFMM_individual_FDR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	−0.0027	549.7338	549.7338	1	15.3180K	3196.9834256	0.0***
sampstrat	0.8382	16.4335	5.4778	3	15.3180K	31.8563530	1.6 × 10−20***
K	−0.0468	8.4059	8.4059	1	15.3180K	48.8845389	2.8 × 10−12***
m	−0.0687	18.1105	18.1105	1	15.3180K	105.3216241	1.2 × 10−24***
phi	−0.0317	3.8567	3.8567	1	15.3180K	22.4287145	2.2 × 10−6***
H	0.0703	18.9143	18.9143	1	15.3180K	109.9965860	1.2 × 10−25***
r	−0.0029	0.0324	0.0324	1	15.3180K	0.1886837	0.66
*** p < 0.001

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - G	0.0073	0.0095	0.7712	0.86748324
EG - R***	−0.0253	0.0095	−2.6713	0.03788814***
EG - T**	−0.0763	0.0095	−8.0517	5.6 × 10−14**
G - R*	−0.0326	0.0095	−3.4424	3.2 × 10−3*
G - T**	−0.0836	0.0095	−8.8220	3.0 × 10−14**
R - T**	−0.0510	0.0095	−5.3819	4.4 × 10−7**
*** p < 0.05
** p < 0.001
* p < 0.01

1.1.3 Megaplots

MEGAPLOT(lfmm_ind, "K.1", colpal = "turbo")

MEGAPLOT(lfmm_ind, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(lfmm_ind, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(lfmm_ind, "TOTALN", colpal = "viridis")

1.1.4 Latent factor versus sample number test

walk(K_plots, grid.arrange)

walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

walk(TOTALN_plots, grid.arrange)

lfmm_ind_fullK <- 
  lfmm_ind_fullK %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge")
  
run_lmer(lfmm_ind_fullK, "TPRCOMBO", filepath = here(p4path, "LFMM_indfullK_TPR.csv"))

## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.

## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.

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## </style>
##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(&gt;F)</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FCFCFC; color: #000000;">0.0002</td>
## <td class="gt_row gt_right">2.2592</td>
## <td class="gt_row gt_right">2.2592</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">284.911850</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.4 &times; 10<sup class='gt_super'>&minus;63</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0995</td>
## <td class="gt_row gt_right">0.2096</td>
## <td class="gt_row gt_right">0.0699</td>
## <td class="gt_row gt_right">3</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">8.812327</td>
## <td class="gt_row gt_right" style="font-weight: bold;">7.8 &times; 10<sup class='gt_super'>&minus;6</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FEEADA; color: #000000;">0.0231</td>
## <td class="gt_row gt_right">2.0491</td>
## <td class="gt_row gt_right">2.0491</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">258.413832</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;57</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FDD3AB; color: #000000;">0.0550</td>
## <td class="gt_row gt_right">11.5739</td>
## <td class="gt_row gt_right">11.5739</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">1459.604079</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.9 &times; 10<sup class='gt_super'>&minus;305</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FAC088; color: #000000;">0.0796</td>
## <td class="gt_row gt_right">24.2608</td>
## <td class="gt_row gt_right">24.2608</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3059.565188</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FABF85; color: #000000;">0.0814</td>
## <td class="gt_row gt_right">25.3972</td>
## <td class="gt_row gt_right">25.3972</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3202.871668</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #EDEAFD; color: #000000;">&minus;0.0148</td>
## <td class="gt_row gt_right">0.8346</td>
## <td class="gt_row gt_right">0.8346</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">105.249242</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.3 &times; 10<sup class='gt_super'>&minus;24</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
##   </tfoot>
## </table>
## </div>
## 
## [[2]]
## <div id="tpzhtafrqn" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
##   <style>html {
##   font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;
## }
## 
## #tpzhtafrqn .gt_table {
##   display: table;
##   border-collapse: collapse;
##   margin-left: auto;
##   margin-right: auto;
##   color: #333333;
##   font-size: 16px;
##   font-weight: normal;
##   font-style: normal;
##   background-color: #FFFFFF;
##   width: auto;
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #A8A8A8;
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##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #A8A8A8;
##   border-left-style: none;
##   border-left-width: 2px;
##   border-left-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_heading {
##   background-color: #FFFFFF;
##   text-align: center;
##   border-bottom-color: #FFFFFF;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_title {
##   color: #333333;
##   font-size: 125%;
##   font-weight: initial;
##   padding-top: 4px;
##   padding-bottom: 4px;
##   padding-left: 5px;
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##   border-bottom-width: 0;
## }
## 
## #tpzhtafrqn .gt_subtitle {
##   color: #333333;
##   font-size: 85%;
##   font-weight: initial;
##   padding-top: 0;
##   padding-bottom: 6px;
##   padding-left: 5px;
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## }
## 
## #tpzhtafrqn .gt_bottom_border {
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_col_headings {
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #D3D3D3;
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## 
## #tpzhtafrqn .gt_col_heading {
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## }
## 
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##   color: #333333;
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## 
## #tpzhtafrqn .gt_column_spanner_outer:first-child {
##   padding-left: 0;
## }
## 
## #tpzhtafrqn .gt_column_spanner_outer:last-child {
##   padding-right: 0;
## }
## 
## #tpzhtafrqn .gt_column_spanner {
##   border-bottom-style: solid;
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## }
## 
## #tpzhtafrqn .gt_group_heading {
##   padding-top: 8px;
##   padding-bottom: 8px;
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##   padding-right: 5px;
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##   background-color: #FFFFFF;
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##   border-bottom-width: 2px;
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##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
##   vertical-align: middle;
## }
## 
## #tpzhtafrqn .gt_empty_group_heading {
##   padding: 0.5px;
##   color: #333333;
##   background-color: #FFFFFF;
##   font-size: 100%;
##   font-weight: initial;
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #D3D3D3;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
##   vertical-align: middle;
## }
## 
## #tpzhtafrqn .gt_from_md > :first-child {
##   margin-top: 0;
## }
## 
## #tpzhtafrqn .gt_from_md > :last-child {
##   margin-bottom: 0;
## }
## 
## #tpzhtafrqn .gt_row {
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
##   padding-right: 5px;
##   margin: 10px;
##   border-top-style: solid;
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##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
##   vertical-align: middle;
##   overflow-x: hidden;
## }
## 
## #tpzhtafrqn .gt_stub {
##   color: #333333;
##   background-color: #FFFFFF;
##   font-size: 100%;
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##   border-right-style: solid;
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##   border-right-color: #D3D3D3;
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##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_stub_row_group {
##   color: #333333;
##   background-color: #FFFFFF;
##   font-size: 100%;
##   font-weight: initial;
##   text-transform: inherit;
##   border-right-style: solid;
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## }
## 
## #tpzhtafrqn .gt_row_group_first td {
##   border-top-width: 2px;
## }
## 
## #tpzhtafrqn .gt_summary_row {
##   color: #333333;
##   background-color: #FFFFFF;
##   text-transform: inherit;
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_first_summary_row {
##   border-top-style: solid;
##   border-top-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_first_summary_row.thick {
##   border-top-width: 2px;
## }
## 
## #tpzhtafrqn .gt_last_summary_row {
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
##   padding-right: 5px;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_grand_summary_row {
##   color: #333333;
##   background-color: #FFFFFF;
##   text-transform: inherit;
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_first_grand_summary_row {
##   padding-top: 8px;
##   padding-bottom: 8px;
##   padding-left: 5px;
##   padding-right: 5px;
##   border-top-style: double;
##   border-top-width: 6px;
##   border-top-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_striped {
##   background-color: rgba(128, 128, 128, 0.05);
## }
## 
## #tpzhtafrqn .gt_table_body {
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #D3D3D3;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_footnotes {
##   color: #333333;
##   background-color: #FFFFFF;
##   border-bottom-style: none;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
##   border-left-style: none;
##   border-left-width: 2px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 2px;
##   border-right-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_footnote {
##   margin: 0px;
##   font-size: 90%;
##   padding-left: 4px;
##   padding-right: 4px;
##   padding-left: 5px;
##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_sourcenotes {
##   color: #333333;
##   background-color: #FFFFFF;
##   border-bottom-style: none;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
##   border-left-style: none;
##   border-left-width: 2px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 2px;
##   border-right-color: #D3D3D3;
## }
## 
## #tpzhtafrqn .gt_sourcenote {
##   font-size: 90%;
##   padding-top: 4px;
##   padding-bottom: 4px;
##   padding-left: 5px;
##   padding-right: 5px;
## }
## 
## #tpzhtafrqn .gt_left {
##   text-align: left;
## }
## 
## #tpzhtafrqn .gt_center {
##   text-align: center;
## }
## 
## #tpzhtafrqn .gt_right {
##   text-align: right;
##   font-variant-numeric: tabular-nums;
## }
## 
## #tpzhtafrqn .gt_font_normal {
##   font-weight: normal;
## }
## 
## #tpzhtafrqn .gt_font_bold {
##   font-weight: bold;
## }
## 
## #tpzhtafrqn .gt_font_italic {
##   font-style: italic;
## }
## 
## #tpzhtafrqn .gt_super {
##   font-size: 65%;
## }
## 
## #tpzhtafrqn .gt_two_val_uncert {
##   display: inline-block;
##   line-height: 1em;
##   text-align: right;
##   font-size: 60%;
##   vertical-align: -0.25em;
##   margin-left: 0.1em;
## }
## 
## #tpzhtafrqn .gt_footnote_marks {
##   font-style: italic;
##   font-weight: normal;
##   font-size: 75%;
##   vertical-align: 0.4em;
## }
## 
## #tpzhtafrqn .gt_asterisk {
##   font-size: 100%;
##   vertical-align: 0;
## }
## 
## #tpzhtafrqn .gt_slash_mark {
##   font-size: 0.7em;
##   line-height: 0.7em;
##   vertical-align: 0.15em;
## }
## 
## #tpzhtafrqn .gt_fraction_numerator {
##   font-size: 0.6em;
##   line-height: 0.6em;
##   vertical-align: 0.45em;
## }
## 
## #tpzhtafrqn .gt_fraction_denominator {
##   font-size: 0.6em;
##   line-height: 0.6em;
##   vertical-align: -0.05em;
## }
## </style>
##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left">EG - G</td>
## <td class="gt_row gt_right" style="background-color: #EAE6FD; color: #000000;">&minus;0.0017</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">&minus;0.8564</td>
## <td class="gt_row gt_right">0.8272429</td></tr>
##     <tr><td class="gt_row gt_left">EG - R</td>
## <td class="gt_row gt_right" style="background-color: #FDF6F0; color: #000000;">0.0008</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">0.3925</td>
## <td class="gt_row gt_right">0.9794972</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - T<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FABF85; color: #000000;">0.0080</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">3.9129</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.3 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left">G - R</td>
## <td class="gt_row gt_right" style="background-color: #FEE8D5; color: #000000;">0.0025</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">1.2489</td>
## <td class="gt_row gt_right">0.5956070</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">G - T<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0097</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">4.7687</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;5</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">R - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC590; color: #000000;">0.0072</td>
## <td class="gt_row gt_right">0.0020</td>
## <td class="gt_row gt_right">3.5208</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.4 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p &lt; 0.01</td>
##     </tr>
##   </tfoot>
## </table>
## </div>

run_lmer(lfmm_ind_fullK, "FDRCOMBO", filepath = here(p4path, "LFMM_indfullK_FDR.csv"))

## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 15330' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 15330)' or larger];
## but be warned that this may result in large computation time and memory use.

## [[1]]
## <div id="fixjlqekcp" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
##   <style>html {
##   font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;
## }
## 
## #fixjlqekcp .gt_table {
##   display: table;
##   border-collapse: collapse;
##   margin-left: auto;
##   margin-right: auto;
##   color: #333333;
##   font-size: 16px;
##   font-weight: normal;
##   font-style: normal;
##   background-color: #FFFFFF;
##   width: auto;
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #A8A8A8;
##   border-right-style: none;
##   border-right-width: 2px;
##   border-right-color: #D3D3D3;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #A8A8A8;
##   border-left-style: none;
##   border-left-width: 2px;
##   border-left-color: #D3D3D3;
## }
## 
## #fixjlqekcp .gt_heading {
##   background-color: #FFFFFF;
##   text-align: center;
##   border-bottom-color: #FFFFFF;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
## }
## 
## #fixjlqekcp .gt_title {
##   color: #333333;
##   font-size: 125%;
##   font-weight: initial;
##   padding-top: 4px;
##   padding-bottom: 4px;
##   padding-left: 5px;
##   padding-right: 5px;
##   border-bottom-color: #FFFFFF;
##   border-bottom-width: 0;
## }
## 
## #fixjlqekcp .gt_subtitle {
##   color: #333333;
##   font-size: 85%;
##   font-weight: initial;
##   padding-top: 0;
##   padding-bottom: 6px;
##   padding-left: 5px;
##   padding-right: 5px;
##   border-top-color: #FFFFFF;
##   border-top-width: 0;
## }
## 
## #fixjlqekcp .gt_bottom_border {
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
## }
## 
## #fixjlqekcp .gt_col_headings {
##   border-top-style: solid;
##   border-top-width: 2px;
##   border-top-color: #D3D3D3;
##   border-bottom-style: solid;
##   border-bottom-width: 2px;
##   border-bottom-color: #D3D3D3;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
##   border-right-width: 1px;
##   border-right-color: #D3D3D3;
## }
## 
## #fixjlqekcp .gt_col_heading {
##   color: #333333;
##   background-color: #FFFFFF;
##   font-size: 100%;
##   font-weight: normal;
##   text-transform: inherit;
##   border-left-style: none;
##   border-left-width: 1px;
##   border-left-color: #D3D3D3;
##   border-right-style: none;
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##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
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##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFC; color: #000000;">&minus;0.0025</td>
## <td class="gt_row gt_right">501.9981</td>
## <td class="gt_row gt_right">501.9981</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">3776.700755</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.5655</td>
## <td class="gt_row gt_right">14.8749</td>
## <td class="gt_row gt_right">4.9583</td>
## <td class="gt_row gt_right">3</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">37.302920</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.2 &times; 10<sup class='gt_super'>&minus;24</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FDF9F6; color: #000000;">0.0220</td>
## <td class="gt_row gt_right">1.8480</td>
## <td class="gt_row gt_right">1.8480</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">13.902783</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.9 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FEF2E9; color: #000000;">0.0711</td>
## <td class="gt_row gt_right">19.3767</td>
## <td class="gt_row gt_right">19.3767</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">145.777616</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.1 &times; 10<sup class='gt_super'>&minus;33</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #F6F5FC; color: #000000;">&minus;0.0329</td>
## <td class="gt_row gt_right">4.1374</td>
## <td class="gt_row gt_right">4.1374</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">31.127031</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.5 &times; 10<sup class='gt_super'>&minus;8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FEEFE2; color: #000000;">0.0974</td>
## <td class="gt_row gt_right">36.3261</td>
## <td class="gt_row gt_right">36.3261</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">273.293640</td>
## <td class="gt_row gt_right" style="font-weight: bold;">7.3 &times; 10<sup class='gt_super'>&minus;61</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #FAF9FC; color: #000000;">&minus;0.0122</td>
## <td class="gt_row gt_right">0.5737</td>
## <td class="gt_row gt_right">0.5737</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">15.3180K</td>
## <td class="gt_row gt_right">4.316443</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.038<sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
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##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left">EG - G</td>
## <td class="gt_row gt_right" style="background-color: #FCFAF7; color: #000000;">0.0024</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">0.2905</td>
## <td class="gt_row gt_right">0.991466</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - R<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #D2CCFD; color: #000000;">&minus;0.0306</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;3.6725</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.4 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #8C8AFC; color: #000000;">&minus;0.0748</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;8.9768</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.7 &times; 10<sup class='gt_super'>&minus;14</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">G - R<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #CFC8FD; color: #000000;">&minus;0.0330</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;3.9628</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.3 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">G - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #8787FC; color: #000000;">&minus;0.0772</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;9.2667</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.3 &times; 10<sup class='gt_super'>&minus;14</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">R - T<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #BEB7FD; color: #000000;">&minus;0.0442</td>
## <td class="gt_row gt_right">0.0083</td>
## <td class="gt_row gt_right">&minus;5.3064</td>
## <td class="gt_row gt_right" style="font-weight: bold;">6.7 &times; 10<sup class='gt_super'>&minus;7</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.01</td>
##     </tr>
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p &lt; 0.001</td>
##     </tr>
##   </tfoot>
## </table>
## </div>

1.2 Site sampling

1.2.1 Summary plots

K

walk(K_plots, grid.arrange)

TPRCOMBO

walk(TPR_plots, grid.arrange)

FDRCOMBO

walk(FDR_plots, grid.arrange)

TOTALN

walk(TOTALN_plots, grid.arrange)

1.1.2 Model summaries

lfmm_site <- 
  lfmm_site %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge") %>%
  filter(K_selection == "tracy.widom")

run_lmer(lfmm_site, "TPRCOMBO", filepath = here(p4path, "LFMM_site_TPR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	−0.0004	0.0593	0.0593	1	8.6090K	8.070827	4.5 × 10−3***
sampstrat	0.0362	0.1180	0.0590	2	8.6090K	8.023909	3.3 × 10−4**
K	0.0160	0.5507	0.5507	1	8.6090K	74.893340	5.9 × 10−18**
m	0.0417	3.7529	3.7529	1	8.6090K	510.419793	7.7 × 10−110**
phi	0.0536	6.1900	6.1900	1	8.6090K	841.869068	1.1 × 10−176**
H	0.0741	11.8217	11.8217	1	8.6090K	1607.807275	1.7 × 10−322**
r	−0.0213	0.9766	0.9766	1	8.6090K	132.822293	1.7 × 10−30**
*** p < 0.01
** p < 0.001

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - EQ	0.0043	0.0023	1.8813	0.14407422
EG - R***	0.0091	0.0023	4.0035	1.8 × 10−4***
EQ - R	0.0048	0.0023	2.1241	0.08499688
*** p < 0.001

run_lmer(lfmm_site, "FDRCOMBO", filepath = here(p4path, "LFMM_site_FDR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	−0.0083	25.3129	25.3129	1	8.6110K	842.37960203	8.7 × 10−177***
sampstrat	1.0906	0.0540	0.0270	2	8.6110K	0.89778252	0.410
K	0.0096	0.1966	0.1966	1	8.6110K	6.54282626	0.011**
m	0.0161	0.5617	0.5617	1	8.6110K	18.69390804	1.6 × 10−5***
phi	−0.0238	1.2192	1.2192	1	8.6110K	40.57304948	2.0 × 10−10***
H	0.0009	0.0018	0.0018	1	8.6110K	0.06058928	0.810
r	0.0036	0.0281	0.0281	1	8.6110K	0.93373450	0.330
*** p < 0.001
** p < 0.05

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - EQ	−0.0061	0.0046	−1.3303	0.3782653
EG - R	−0.0024	0.0046	−0.5263	0.8584367
EQ - R	0.0037	0.0046	0.8037	0.7007541

1.2.3 Megaplots

MEGAPLOT(lfmm_site, "K.1", colpal = "turbo")

MEGAPLOT(lfmm_site, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(lfmm_site, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(lfmm_site, "TOTALN", colpal = "viridis")

1.2.4 Latent factor versus sample number test

walk(K_plots, grid.arrange)

walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

walk(TOTALN_plots, grid.arrange) 

lfmm_site_fullK <- 
  lfmm_site_fullK %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(method == "ridge")
  
run_lmer(lfmm_site_fullK, "TPRCOMBO", filepath = here(p4path, "LFMM_sitefullK_TPR.csv"))

## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.

## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.

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##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(&gt;F)</th>
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##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #F9F9FC; color: #000000;">&minus;0.0018</td>
## <td class="gt_row gt_right">1.1952</td>
## <td class="gt_row gt_right">1.1952</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">183.240394</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.5 &times; 10<sup class='gt_super'>&minus;41</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #FEE6D1; color: #000000;">0.0191</td>
## <td class="gt_row gt_right">0.0892</td>
## <td class="gt_row gt_right">0.0446</td>
## <td class="gt_row gt_right">2</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">6.835991</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FEEBDA; color: #000000;">0.0152</td>
## <td class="gt_row gt_right">0.4970</td>
## <td class="gt_row gt_right">0.4970</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">76.192821</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.1 &times; 10<sup class='gt_super'>&minus;18</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FDD0A5; color: #000000;">0.0389</td>
## <td class="gt_row gt_right">3.2589</td>
## <td class="gt_row gt_right">3.2589</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">499.649532</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.3 &times; 10<sup class='gt_super'>&minus;107</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FCCA9A; color: #000000;">0.0442</td>
## <td class="gt_row gt_right">4.2123</td>
## <td class="gt_row gt_right">4.2123</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">645.825647</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.9 &times; 10<sup class='gt_super'>&minus;137</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0656</td>
## <td class="gt_row gt_right">9.2807</td>
## <td class="gt_row gt_right">9.2807</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1422.900812</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.6 &times; 10<sup class='gt_super'>&minus;288</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">r</td>
## <td class="gt_row gt_right" style="background-color: #DBD6FD; color: #000000;">&minus;0.0206</td>
## <td class="gt_row gt_right">0.9155</td>
## <td class="gt_row gt_right">0.9155</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">140.355642</td>
## <td class="gt_row gt_right" style="font-weight: bold;">4.0 &times; 10<sup class='gt_super'>&minus;32</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
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##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="5" class="gt_heading gt_title gt_font_normal" style>Tukey test</th>
##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Estimate</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Z ratio</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">p</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - EQ<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC48F; color: #000000;">0.0057</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">2.6691</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.02077436<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - R<sup class="gt_footnote_marks gt_asterisk">**</sup></td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">0.0076</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">3.5508</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;3</sup><sup class="gt_footnote_marks gt_asterisk">**</sup></td></tr>
##     <tr><td class="gt_row gt_left">EQ - R</td>
## <td class="gt_row gt_right" style="background-color: #FEE9D7; color: #000000;">0.0019</td>
## <td class="gt_row gt_right">0.0021</td>
## <td class="gt_row gt_right">0.8835</td>
## <td class="gt_row gt_right">0.65075396</td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.05</td>
##     </tr>
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">**</sup> p &lt; 0.01</td>
##     </tr>
##   </tfoot>
## </table>
## </div>

run_lmer(lfmm_site_fullK, "FDRCOMBO", filepath = here(p4path, "LFMM_sitefullK_FDR.csv"))

## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'pbkrtest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(pbkrtest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.
## Note: D.f. calculations have been disabled because the number of observations exceeds 3000.
## To enable adjustments, add the argument 'lmerTest.limit = 8620' (or larger)
## [or, globally, 'set emm_options(lmerTest.limit = 8620)' or larger];
## but be warned that this may result in large computation time and memory use.

## [[1]]
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##   <table class="gt_table">
##   <thead class="gt_header">
##     <tr>
##       <th colspan="8" class="gt_heading gt_title gt_font_normal" style>Linear mixed effect model</th>
##     </tr>
##     <tr>
##       <th colspan="8" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)</em></th>
##     </tr>
##   </thead>
##   <thead class="gt_col_headings">
##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Predictors</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Fixed Effects</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Sum Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Mean Sq</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">NumDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">DenDF</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">F value</th>
##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Pr(&gt;F)</th>
##     </tr>
##   </thead>
##   <tbody class="gt_table_body">
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">nsamp</td>
## <td class="gt_row gt_right" style="background-color: #FAFAFC; color: #000000;">&minus;0.0187</td>
## <td class="gt_row gt_right">129.4249</td>
## <td class="gt_row gt_right">129.4249</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1992.658631</td>
## <td class="gt_row gt_right" style="font-weight: bold;">0.0<sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">sampstrat</td>
## <td class="gt_row gt_right" style="background-color: #F6B26B; color: #000000;">1.2219</td>
## <td class="gt_row gt_right">2.3866</td>
## <td class="gt_row gt_right">1.1933</td>
## <td class="gt_row gt_right">2</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">18.372105</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.1 &times; 10<sup class='gt_super'>&minus;8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">K</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFA; color: #000000;">0.0190</td>
## <td class="gt_row gt_right">0.7755</td>
## <td class="gt_row gt_right">0.7755</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">11.939477</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.5 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">m</td>
## <td class="gt_row gt_right" style="background-color: #FCFBFA; color: #000000;">0.0196</td>
## <td class="gt_row gt_right">0.8298</td>
## <td class="gt_row gt_right">0.8298</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">12.776418</td>
## <td class="gt_row gt_right" style="font-weight: bold;">3.5 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">phi</td>
## <td class="gt_row gt_right" style="background-color: #FAFAFC; color: #000000;">&minus;0.0191</td>
## <td class="gt_row gt_right">0.7830</td>
## <td class="gt_row gt_right">0.7830</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">12.054888</td>
## <td class="gt_row gt_right" style="font-weight: bold;">5.2 &times; 10<sup class='gt_super'>&minus;4</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">H</td>
## <td class="gt_row gt_right" style="background-color: #FCFAF7; color: #000000;">0.0389</td>
## <td class="gt_row gt_right">3.2570</td>
## <td class="gt_row gt_right">3.2570</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6091K</td>
## <td class="gt_row gt_right">50.145685</td>
## <td class="gt_row gt_right" style="font-weight: bold;">1.5 &times; 10<sup class='gt_super'>&minus;12</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left">r</td>
## <td class="gt_row gt_right" style="background-color: #FCFCFB; color: #000000;">0.0065</td>
## <td class="gt_row gt_right">0.0916</td>
## <td class="gt_row gt_right">0.0916</td>
## <td class="gt_row gt_right">1</td>
## <td class="gt_row gt_right">8.6090K</td>
## <td class="gt_row gt_right">1.410227</td>
## <td class="gt_row gt_right">0.24</td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
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##       <td class="gt_footnote" colspan="8"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
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##     </tr>
##     <tr>
##       <th colspan="5" class="gt_heading gt_subtitle gt_font_normal gt_bottom_border" style><em>pairwise ~ sampstrat</em></th>
##     </tr>
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##     <tr>
##       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Contrast</th>
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##       <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">SE</th>
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##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EG - EQ<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #FBC28B; color: #000000;">0.0301</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">4.4781</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.2 &times; 10<sup class='gt_super'>&minus;5</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##     <tr><td class="gt_row gt_left">EG - R</td>
## <td class="gt_row gt_right" style="background-color: #E5E1FD; color: #000000;">&minus;0.0087</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">&minus;1.2978</td>
## <td class="gt_row gt_right">0.396384</td></tr>
##     <tr><td class="gt_row gt_left" style="font-weight: bold;">EQ - R<sup class="gt_footnote_marks gt_asterisk">***</sup></td>
## <td class="gt_row gt_right" style="background-color: #8787FC; color: #000000;">&minus;0.0388</td>
## <td class="gt_row gt_right">0.0067</td>
## <td class="gt_row gt_right">&minus;5.7761</td>
## <td class="gt_row gt_right" style="font-weight: bold;">2.3 &times; 10<sup class='gt_super'>&minus;8</sup><sup class="gt_footnote_marks gt_asterisk">***</sup></td></tr>
##   </tbody>
##   
##   <tfoot class="gt_footnotes">
##     <tr>
##       <td class="gt_footnote" colspan="5"><sup class="gt_footnote_marks gt_asterisk">***</sup> p &lt; 0.001</td>
##     </tr>
##   </tfoot>
## </table>
## </div>

2. RDA

2.1 Individual sampling

2.1.1 Summary plots

rda_ind <- format_rda(here(p3path, "rda_indsampling_results.csv"))
rda_ind_tidy <- 
  rda_ind %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  group_by(correctPC) %>%
  group_split()

walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

2.1.2 Model summaries

rda_ind <- 
  rda_ind %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(correctPC == "FALSE") 

run_lmer(rda_ind, "TPRCOMBO", filepath = here(p4path, "RDA_individual_TPR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	0.0002	2.8394	2.8394	1	15.3480K	545.389450	1.5 × 10−118***
sampstrat	0.0875	0.3001	0.1000	3	15.3480K	19.211563	2.0 × 10−12***
K	0.0165	1.0439	1.0439	1	15.3480K	200.509665	3.1 × 10−45***
m	0.0438	7.3555	7.3555	1	15.3480K	1412.856406	7.2 × 10−296***
phi	0.0440	7.4213	7.4213	1	15.3480K	1425.494641	2.2 × 10−298***
H	0.0436	7.2900	7.2900	1	15.3480K	1400.274445	2.3 × 10−293***
r	0.0036	0.0488	0.0488	1	15.3480K	9.371404	2.2 × 10−3**
*** p < 0.001
** p < 0.01

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - G	0.0005	0.0016	0.2768	0.9926010
EG - R	0.0029	0.0016	1.7594	0.2931233
EG - T***	0.0110	0.0016	6.6817	1.4 × 10−10***
G - R	0.0024	0.0016	1.4826	0.4480091
G - T***	0.0105	0.0016	6.4050	9.0 × 10−10***
R - T***	0.0081	0.0016	4.9224	5.1 × 10−6***
*** p < 0.001

run_lmer(rda_ind, "FDRCOMBO", filepath = here(p4path, "RDA_individual_FDR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	0.0003	5.7961	5.7961	1	15.3480K	373.268676	3.4 × 10−82***
sampstrat	0.1162	0.2103	0.0701	3	15.3480K	4.515102	3.6 × 10−3**
K	0.0153	0.9004	0.9004	1	15.3480K	57.987784	2.8 × 10−14***
m	0.0753	21.8007	21.8007	1	15.3480K	1403.969867	4.2 × 10−294***
phi	0.0647	16.0600	16.0600	1	15.3480K	1034.264854	1.2 × 10−219***
H	0.0610	14.2799	14.2799	1	15.3480K	919.628150	3.1 × 10−196***
r	0.0091	0.3176	0.3176	1	15.3480K	20.451012	6.2 × 10−6***
*** p < 0.001
** p < 0.01

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - G	−0.0010	0.0028	−0.3555	0.98460216
EG - R	0.0020	0.0028	0.6959	0.89870855
EG - T***	0.0085	0.0028	2.9888	0.01487071***
G - R	0.0030	0.0028	1.0514	0.71907362
G - T**	0.0095	0.0028	3.3443	4.6 × 10−3**
R - T	0.0065	0.0028	2.2929	0.09963697
*** p < 0.05
** p < 0.01

1.1.3 Megaplots

MEGAPLOT(rda_ind, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(rda_ind, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(rda_ind, "TOTALN", colpal = "viridis")

2.2 Site sampling

2.2.1 Summary plots

rda_site <- format_rda(here(p3path, "rda_sitesampling_results.csv")) 
rda_site_tidy <- 
  rda_site %>%
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  group_by(correctPC) %>%
  group_split()

walk(TPR_plots, grid.arrange)

walk(FDR_plots, grid.arrange)

walk(TOTALN_plots, grid.arrange)

2.2.2 Model summaries

rda_site <- 
  rda_site %>% 
  filter(padj == "fdr") %>%
  filter(sig == 0.05) %>%
  filter(correctPC == "FALSE") 

run_lmer(rda_site, "TPRCOMBO", filepath = here(p4path, "RDA_site_TPR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	0.0015	0.8335	0.8335	1	8.6290K	232.154396	9.5 × 10−52***
sampstrat	0.0717	0.1133	0.0567	2	8.6290K	15.782322	1.4 × 10−7***
K	0.0173	0.6489	0.6489	1	8.6290K	180.732574	8.6 × 10−41***
m	0.0322	2.2403	2.2403	1	8.6290K	623.983518	5.0 × 10−133***
phi	0.0321	2.2322	2.2322	1	8.6290K	621.743005	1.4 × 10−132***
H	0.0315	2.1447	2.1447	1	8.6290K	597.363316	1.3 × 10−127***
r	0.0019	0.0081	0.0081	1	8.6290K	2.261166	0.13
*** p < 0.001

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - EQ	−0.0001	0.0016	−0.0550	0.9983351
EG - R***	0.0076	0.0016	4.8378	3.9 × 10−6***
EQ - R***	0.0077	0.0016	4.8928	3.0 × 10−6***
*** p < 0.001

run_lmer(rda_site, "FDRCOMBO", filepath = here(p4path, "RDA_site_FDR.csv"))

[[1]]

Linear mixed effect model
statistic ~ nsamp + sampstrat + K + m + phi + H + r + (1 | seed)
Predictors	Fixed Effects	Sum Sq	Mean Sq	NumDF	DenDF	F value	Pr(>F)
nsamp	0.0018	1.1681	1.1681	1	8.6290K	140.00975	4.7 × 10−32***
sampstrat	0.0845	0.1085	0.0542	2	8.6290K	6.50242	1.5 × 10−3**
K	0.0133	0.3801	0.3801	1	8.6290K	45.55864	1.6 × 10−11***
m	0.0378	3.0791	3.0791	1	8.6290K	369.07182	1.4 × 10−80***
phi	0.0336	2.4370	2.4370	1	8.6290K	292.10683	2.0 × 10−64***
H	0.0297	1.8994	1.8994	1	8.6290K	227.67214	8.5 × 10−51***
r	0.0144	0.4449	0.4449	1	8.6290K	53.32587	3.1 × 10−13***
*** p < 0.001
** p < 0.01

[[2]]

Tukey test
pairwise ~ sampstrat
Contrast	Estimate	SE	Z ratio	p
EG - EQ***	0.0057	0.0024	2.3728	0.04642683***
EG - R**	0.0085	0.0024	3.5382	1.2 × 10−3**
EQ - R	0.0028	0.0024	1.1654	0.47395300
*** p < 0.05
** p < 0.01

2.2.3 Megaplots

MEGAPLOT(rda_site, "TPRCOMBO", colpal = "plasma")

MEGAPLOT(rda_site, "FDRCOMBO", colpal = "viridis", direction = -1)

MEGAPLOT(rda_site, "TOTALN", colpal = "viridis")

Figures

arrange_figures(lfmm_ind, rda_ind, "FDR", 
                "A. LFMM", "B. RDA",
                colpal = "viridis", direction = -1, dig = 2, maxv = 0.86, minv = 0)

arrange_figures(lfmm_ind, rda_ind, "TPR", 
                "A. LFMM", "B. RDA",
                colpal = "plasma", direction = 1, dig = 2, minv = 0, maxv = 0.17)

arrange_figures(lfmm_site, rda_site, "TPR", 
                "A. LFMM", "B. RDA",
                colpal = "plasma", direction = 1, dig = 2, minv = 0, maxv = 0.11)

arrange_figures(lfmm_site, rda_site, "FDR", 
                "A. LFMM", "B. RDA",
                colpal = "viridis", direction = -1, dig = 2, maxv = 1, minv = 0)